ProSeg: a database of local structures of protein segments.
Integration of knowledge on the sequence-structure correlation of proteins provides a basis for the structural design of artificial novel proteins. As one of strategies, it is effective to consider a short segment, whose size is in between an amino acid and a domain, as a correlation unit for exploring the structure-to-sequence relationship. Here we report the development of a database called ProSeg, which consists of two sub-databases, Segment DB and Cluster DB. Segment DB contains tens of thousands of segments that were prepared by dividing the primary sequences of 370 proteins using a sliding L-residue window (L = 5, 9, 11, 15). These segments were classified into several thousands of clusters according to their three-dimensional structural resemblance. Cluster DB contains much cluster-related information, which includes image, rank, frequency, secondary structure assignment, sequence profile, etc. Users can search for a suitable cluster by inputting an appropriate parameter (i.e., PDB ID, dihedral angles, or DSSP symbols), which identifies the backbone structure of a query segment. Analogous to a language, ProSeg could be regarded as a 'structure-sequence dictionary' that contains over 10,000 'protein words'. ProSeg is freely accessible through the Internet ( http://riodb.ibase.aist.go.jp/proseg/ ).
Sawada
Yoshito
Y
National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Tsukuba 305-8566, Japan.
Honda
Shinya
S
D000595:Amino Acid Sequence; D016000:Cluster Analysis; D030562:Databases, Protein; D020407:Internet; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D011506:Proteins